1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
|
/*
* utils.c
*
* Utility stuff
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#include <math.h>
#include <string.h>
#include <stdio.h>
#include "utils.h"
#include "image.h"
size_t skipspace(const char *s)
{
size_t i;
for ( i=0; i<strlen(s); i++ ) {
if ( (s[i] != ' ') && (s[i] != '\t') ) return i;
}
return strlen(s);
}
void chomp(char *s)
{
size_t i;
if ( !s ) return;
for ( i=0; i<strlen(s); i++ ) {
if ( (s[i] == '\n') || (s[i] == '\r') ) {
s[i] = '\0';
return;
}
}
}
void progress_bar(int val, int total, const char *text)
{
double frac;
int n, i;
char s[1024];
const int width = 50;
frac = (double)val/total;
n = (int)(frac*width);
for ( i=0; i<n; i++ ) s[i] = '=';
for ( i=n; i<width; i++ ) s[i] = '.';
s[width] = '\0';
STATUS("\r%s: |%s|", text, s);
if ( val == total ) STATUS("\n");
fflush(stdout);
}
static int fake_poisson_noise(double expected)
{
double x1, x2, w;
double noise, rf;
do {
x1 = 2.0 * ((double)random()/RAND_MAX) - 1.0;
x2 = 2.0 * ((double)random()/RAND_MAX) - 1.0;
w = pow(x1, 2.0) + pow(x2, 2.0);
} while ( w >= 1.0 );
w = sqrt((-2.0*log(w))/w);
noise = w * x1;
rf = expected + noise*sqrt(expected);
return (int)rf;
}
int poisson_noise(double expected)
{
double L;
int k = 0;
double p = 1.0;
/* For large values of the mean, we get big problems with arithmetic.
* In such cases, fall back on a Gaussian with the right variance. */
if ( expected > 100.0 ) return fake_poisson_noise(expected);
L = exp(-expected);
do {
double r;
k++;
r = (double)random()/(double)RAND_MAX;
p *= r;
} while ( p > L );
return k - 1;
}
double quaternion_modulus(struct quaternion q)
{
return sqrt(q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z);
}
struct quaternion normalise_quaternion(struct quaternion q)
{
double mod;
struct quaternion r;
mod = quaternion_modulus(q);
r.w = q.w / mod;
r.x = q.x / mod;
r.y = q.y / mod;
r.z = q.z / mod;
return r;
}
struct quaternion random_quaternion()
{
struct quaternion q;
q.w = 2.0*(double)random()/RAND_MAX - 1.0;
q.x = 2.0*(double)random()/RAND_MAX - 1.0;
q.y = 2.0*(double)random()/RAND_MAX - 1.0;
q.z = 2.0*(double)random()/RAND_MAX - 1.0;
q = normalise_quaternion(q);
return q;
}
int quaternion_valid(struct quaternion q)
{
double qmod;
qmod = quaternion_modulus(q);
/* Modulus = 1 to within some tolerance?
* Nasty allowance for floating-point accuracy follows... */
if ( (qmod > 0.999) && (qmod < 1.001) ) return 1;
return 0;
}
struct rvec quat_rot(struct rvec q, struct quaternion z)
{
struct rvec res;
double t01, t02, t03, t11, t12, t13, t22, t23, t33;
t01 = z.w*z.x;
t02 = z.w*z.y;
t03 = z.w*z.z;
t11 = z.x*z.x;
t12 = z.x*z.y;
t13 = z.x*z.z;
t22 = z.y*z.y;
t23 = z.y*z.z;
t33 = z.z*z.z;
res.u = (1.0 - 2.0 * (t22 + t33)) * q.u
+ (2.0 * (t12 + t03)) * q.v
+ (2.0 * (t13 - t02)) * q.w;
res.v = (2.0 * (t12 - t03)) * q.u
+ (1.0 - 2.0 * (t11 + t33)) * q.v
+ (2.0 * (t01 + t23)) * q.w;
res.w = (2.0 * (t02 + t13)) * q.u
+ (2.0 * (t23 - t01)) * q.v
+ (1.0 - 2.0 * (t11 + t22)) * q.w;
return res;
}
|
